Human-mouse comparison of the insertion sites in BCP-ALL cases
| Mouse gene with insertion . | Insertion location (relative to gene) . | No. unique insertions . | Dysregulation of gene in human ETV6-RUNX1 ALL lesions . | Reference . |
|---|---|---|---|---|
| Ikzf1 | Coding | 4 | In a deletion region | 36 *,31 † |
| C20orf94 | Coding | 3 | In a deletion region | 7 |
| Ebf1 | Coding | 3 | In a deletion region | 7,8 |
| Fhit | Coding | 3 | In a deletion region | 7 |
| Chn2 | Coding | 2 | Down-regulated expression | 37 |
| Epor | Promoter | 2 | Up-regulated expression | 32,37,38 |
| Flt3 | Promoter | 2 | Activating mutations | 39 |
| Mllt3 | Coding | 2 | In a deletion region | 7 |
| Nf1 | Coding | 2 | In a deletion region | 7 |
| Smarcc1 | Coding | 2 | In a deletion region | 24 |
| Tbl1xr1 | Coding | 2 | In a deletion region | 7,8 |
| Tcf4 (E2–2) | Coding | 2 | In a deletion region | 36,40 |
| Ankrd27 | Coding | 1 | In a deletion region | 24 |
| Arid1b | Coding | 1 | In a deletion region | 41 |
| Atf2 | Coding | 1 | Down-regulated expression | 37 |
| Atp10a | Coding | 1 | In a deletion region | 41 |
| B4galt1 | Coding | 1 | Down-regulated expression | 37 |
| Birc7 | Promoter | 1 | Up-regulated expression | 38 |
| Cd44 | Coding | 1 | Down-regulated expression | 32,37,38 |
| Clic5 | Coding | 1 | Up-regulated expression | 38 |
| Dpf3 | Coding | 1 | In a deletion region | 7 |
| Eif2s1 | Coding | 1 | Down-regulated expression | 37 |
| Fbn2 | Coding | 1 | Up-regulated expression | 38 |
| Flnb | Coding | 1 | Down-regulated expression | 37 |
| Fyn | Coding | 1 | In a deletion region | 36 * |
| Grik2 | Coding | 1 | In a deletion region | 7 |
| Hmg20a | Coding | 1 | Up-regulated expression | 38 |
| Jak1 | Coding | 1 | Expression up-regulated | 37 |
| Lef1 | Coding | 1 | In a deletion region | 7 |
| Lztfl1 | Coding | 1 | In a deletion region | 24 |
| Myo10 | Coding | 1 | Up-regulated expression | 38 |
| Nr3c1 | Coding | 1 | In a deletion region | 7 |
| Nr3c2 | Coding | 1 | In a deletion region | 7 |
| Pbef1 (Nampt) | Coding | 1 | In a deletion region | 36 |
| Pde4b | Coding | 1 | In a deletion region | 40 |
| Pdlim1 | Coding | 1 | Down-regulated expression | 37 |
| Ptpn2 | Coding | 1 | Down-regulated expression | 37 |
| Ptprk | Coding | 1 | Up-regulated expression | 37,38 |
| Rap1b | Coding | 1 | In a deletion region | 41 |
| Rb1 | Coding | 1 | In a deletion region | 7,8 |
| Rhpn2 | Promoter | 1 | In a deletion region | 24 |
| Tcf3 (E2A) | Promoter | 1 | In a deletion region | 36 * |
| Tcf12 | Coding | 1 | In a deletion region | 41 |
| Thada | Coding | 1 | In a deletion region | 7 |
| Usp9x | Coding | 1 | Down-regulated expression | 37 |
| Yipf7 | Coding | 1 | In a deletion region | 40 |
| Ywhaq | Coding | 1 | In a deletion region | 40 |
| Zcchc7 | Coding | 1 | In a deletion region | 8,24 |
| Mouse gene with insertion . | Insertion location (relative to gene) . | No. unique insertions . | Dysregulation of gene in human ETV6-RUNX1 ALL lesions . | Reference . |
|---|---|---|---|---|
| Ikzf1 | Coding | 4 | In a deletion region | 36 *,31 † |
| C20orf94 | Coding | 3 | In a deletion region | 7 |
| Ebf1 | Coding | 3 | In a deletion region | 7,8 |
| Fhit | Coding | 3 | In a deletion region | 7 |
| Chn2 | Coding | 2 | Down-regulated expression | 37 |
| Epor | Promoter | 2 | Up-regulated expression | 32,37,38 |
| Flt3 | Promoter | 2 | Activating mutations | 39 |
| Mllt3 | Coding | 2 | In a deletion region | 7 |
| Nf1 | Coding | 2 | In a deletion region | 7 |
| Smarcc1 | Coding | 2 | In a deletion region | 24 |
| Tbl1xr1 | Coding | 2 | In a deletion region | 7,8 |
| Tcf4 (E2–2) | Coding | 2 | In a deletion region | 36,40 |
| Ankrd27 | Coding | 1 | In a deletion region | 24 |
| Arid1b | Coding | 1 | In a deletion region | 41 |
| Atf2 | Coding | 1 | Down-regulated expression | 37 |
| Atp10a | Coding | 1 | In a deletion region | 41 |
| B4galt1 | Coding | 1 | Down-regulated expression | 37 |
| Birc7 | Promoter | 1 | Up-regulated expression | 38 |
| Cd44 | Coding | 1 | Down-regulated expression | 32,37,38 |
| Clic5 | Coding | 1 | Up-regulated expression | 38 |
| Dpf3 | Coding | 1 | In a deletion region | 7 |
| Eif2s1 | Coding | 1 | Down-regulated expression | 37 |
| Fbn2 | Coding | 1 | Up-regulated expression | 38 |
| Flnb | Coding | 1 | Down-regulated expression | 37 |
| Fyn | Coding | 1 | In a deletion region | 36 * |
| Grik2 | Coding | 1 | In a deletion region | 7 |
| Hmg20a | Coding | 1 | Up-regulated expression | 38 |
| Jak1 | Coding | 1 | Expression up-regulated | 37 |
| Lef1 | Coding | 1 | In a deletion region | 7 |
| Lztfl1 | Coding | 1 | In a deletion region | 24 |
| Myo10 | Coding | 1 | Up-regulated expression | 38 |
| Nr3c1 | Coding | 1 | In a deletion region | 7 |
| Nr3c2 | Coding | 1 | In a deletion region | 7 |
| Pbef1 (Nampt) | Coding | 1 | In a deletion region | 36 |
| Pde4b | Coding | 1 | In a deletion region | 40 |
| Pdlim1 | Coding | 1 | Down-regulated expression | 37 |
| Ptpn2 | Coding | 1 | Down-regulated expression | 37 |
| Ptprk | Coding | 1 | Up-regulated expression | 37,38 |
| Rap1b | Coding | 1 | In a deletion region | 41 |
| Rb1 | Coding | 1 | In a deletion region | 7,8 |
| Rhpn2 | Promoter | 1 | In a deletion region | 24 |
| Tcf3 (E2A) | Promoter | 1 | In a deletion region | 36 * |
| Tcf12 | Coding | 1 | In a deletion region | 41 |
| Thada | Coding | 1 | In a deletion region | 7 |
| Usp9x | Coding | 1 | Down-regulated expression | 37 |
| Yipf7 | Coding | 1 | In a deletion region | 40 |
| Ywhaq | Coding | 1 | In a deletion region | 40 |
| Zcchc7 | Coding | 1 | In a deletion region | 8,24 |
The Ensembl mouse genome annotation database (version 59) was used to find the associated mouse gene for the human genes relevant to ETV6-RUNX1 patients (genes that did not map were hand-curated). The location of insertion sites was scored as being in the coding region of the gene (“coding”) or ≤ 5K upstream of the gene (“promoter”).
Reported in childhood ALL (not necessarily ETV6-RUNX1–positive patients).
IKZF1 deletion outside of the BCR-ABL context.